From 679cf716192cdfd91dfd232578cbd4e30d7eac12 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 15 Nov 2022 08:01:52 +0100 Subject: Import saemix for easier profiling, update online docs --- docs/dev/articles/web_only/benchmarks.html | 29 +++++++++++++----------- docs/dev/articles/web_only/saem_benchmarks.html | 29 +++++++++++++----------- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/Rplot001.png | Bin 1011 -> 22432 bytes docs/dev/reference/logLik.saem.mmkin.html | 5 +++- docs/dev/reference/mkinpredict.html | 13 +++++++---- docs/dev/reference/saem.html | 11 +++++---- 7 files changed, 52 insertions(+), 37 deletions(-) (limited to 'docs') diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index cb048453..5c7aa3dc 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -78,7 +78,10 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
    • @@ -109,7 +112,7 @@

    Benchmark timings for mkin

    Johannes Ranke

    -

    Last change 14 July 2022 (rebuilt 2022-11-14)

    +

    Last change 14 July 2022 (rebuilt 2022-11-15)

    Source: vignettes/web_only/benchmarks.rmd @@ -348,8 +351,8 @@ Ryzen 7 1700 4.2.2 1.2.0 -2.030 -3.791 +2.129 +3.784 @@ -527,9 +530,9 @@ Ryzen 7 1700 4.2.2 1.2.0 -1.579 -6.591 -3.107 +1.559 +6.097 +2.841 @@ -761,12 +764,12 @@ Ryzen 7 1700 4.2.2 1.2.0 -0.915 -1.426 -1.613 -3.224 -2.068 -2.962 +0.911 +1.328 +1.519 +2.986 +1.957 +2.769 diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html index 97ea6fd4..e54bc38c 100644 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ b/docs/dev/articles/web_only/saem_benchmarks.html @@ -78,7 +78,10 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
    • @@ -109,7 +112,7 @@

    Benchmark timings for saem.mmkin

    Johannes Ranke

    -

    Last change 14 November 2022 (rebuilt 2022-11-14)

    +

    Last change 14 November 2022 (rebuilt 2022-11-15)

    Source: vignettes/web_only/saem_benchmarks.rmd @@ -306,10 +309,10 @@ Linux 1.2.0 3.2 -2.589 -4.945 -4.786 -4.484 +2.11 +4.632 +4.264 +4.93

    Two-component error fits for SFO, DFOP, SFORB and HS.

    @@ -329,10 +332,10 @@ Linux 1.2.0 3.2 -5.645 -8.115 -7.737 -7.782 +5.602 +7.373 +7.815 +7.831 @@ -354,8 +357,8 @@ Linux 1.2.0 3.2 -25.921 -766.034 +24.014 +749.699 @@ -376,7 +379,7 @@ Linux 1.2.0 3.2 -1269.799 +1249.834 diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index ad0d8b19..e0c11a84 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -13,7 +13,7 @@ articles: dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html saem_benchmarks: web_only/saem_benchmarks.html -last_built: 2022-11-14T20:49Z +last_built: 2022-11-14T23:45Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png index 17a35806..b3448db0 100644 Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html index b1ea22ef..ebef3b10 100644 --- a/docs/dev/reference/logLik.saem.mmkin.html +++ b/docs/dev/reference/logLik.saem.mmkin.html @@ -59,7 +59,10 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html index 14f2b75b..37930912 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -61,7 +61,10 @@ kinetic parameters and initial values for the state variables.">Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -371,10 +374,10 @@ as these always return mapped output.

    } #> Loading required package: rbenchmark #> test relative elapsed -#> 2 deSolve_compiled 1.00 0.004 -#> 4 analytical 5.25 0.021 -#> 1 eigen 6.00 0.024 -#> 3 deSolve 52.50 0.210 +#> 2 deSolve_compiled 1.0 0.005 +#> 1 eigen 4.2 0.021 +#> 4 analytical 4.2 0.021 +#> 3 deSolve 40.8 0.204 # \dontrun{ # Predict from a fitted model diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 968dc68c..73382cba 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -61,7 +61,10 @@ Expectation Maximisation algorithm (SAEM).">Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -429,8 +432,8 @@ using mmkin.

    #> saemix version used for fitting: 3.2 #> mkin version used for pre-fitting: 1.2.0 #> R version used for fitting: 4.2.2 -#> Date of fit: Mon Nov 14 21:06:30 2022 -#> Date of summary: Mon Nov 14 21:06:30 2022 +#> Date of fit: Tue Nov 15 00:45:58 2022 +#> Date of summary: Tue Nov 15 00:45:58 2022 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -445,7 +448,7 @@ using mmkin.

    #> #> Model predictions using solution type analytical #> -#> Fitted in 9.625 s +#> Fitted in 9.189 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Constant variance -- cgit v1.2.1